3DH2

Crystal structure of ribonuclease Sa2 with guanosine-3'-cyclophosphate prepared by cocrystallization

• PDB DOI: https://doi.org/10.2210/pdb3DH2/pdb

• Classification: HYDROLASE
• Organism(s): Kitasatospora aureofaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-16 Released: 2009-06-16 
• Deposition Author(s): Sevcik, J., Bauerova-Hlinkova, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.259 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.73 kDa 
• Atom Count: 3,314 
• Modelled Residue Count: 380 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease	A, B, C, D	97	Kitasatospora aureofaciens	Mutation(s): 0
UniProt
Find proteins for Q53752 (Kitasatospora aureofaciens) Explore Q53752  Go to UniProtKB:  Q53752

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3GP	G [auth A], I [auth B], K [auth C], L [auth D]	GUANOSINE-3'-MONOPHOSPHATE C10 H14 N5 O8 P ZDPUTNZENXVHJC-UUOKFMHZSA-N
BGC	E [auth A], H [auth B], J [auth C]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.259 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.192	α = 90
b = 62.648	β = 129.18
c = 68.299	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Sevcik, J., Bauerova-Hlinkova, V.

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary